A Dense Genetic Linkage Map for Common Carp and Its Integration with a BAC-Based Physical Map

Abstract

BackgroundCommon carp (Cyprinus carpio) is one of the most important aquaculture species with an annual global production of 3.4 million metric tons. It is also an important ornamental species as well as an important model species for aquaculture research. To improve the economically important traits of this fish, a number of genomic resources and genetic tools have been developed, including several genetic maps and a bacterial artificial chromosome (BAC)-based physical map. However, integrated genetic and physical maps are not available to study quantitative trait loci (QTL) and assist with fine mapping, positional cloning and whole genome sequencing and assembly. The objective of this study was to integrate the currently available BAC-based physical and genetic maps.ResultsThe genetic map was updated with 592 novel markers, including 312 BAC-anchored microsatellites and 130 SNP markers, and contained 1,209 genetic markers on 50 linkage groups, spanning 3,565.9 cM in the common carp genome. An integrated genetic and physical map of the common carp genome was then constructed, which was composed of 463 physical map contigs and 88 single BACs. Combined lengths of the contigs and single BACs covered a physical length of 498.75 Mb, or around 30% of the common carp genome. Comparative analysis between common carp and zebrafish genomes was performed based on the integrated map, providing more insights into the common carp specific whole genome duplication and segmental rearrangements in the genome.ConclusionWe integrated a BAC-based physical map to a genetic linkage map of common carp by anchoring BAC-associated genetic markers. The density of the genetic linkage map was significantly increased. The integrated map provides a tool for both genetic and genomic studies of common carp, which will help us to understand the genomic architecture of common carp and facilitate fine mapping and positional cloning of economically important traits for genetic improvement and modification.

Microsatellite-centromere mapping in common carp through half-tetrad analysis in diploid meiogynogenetic families

“…The estimated speciation time between common carp and zebrafish was 100 to 120 Mya, as predicted by individual genes and transcriptome analysis (Kruiswijk et al 2002;Wang et al 2012). Comparative genome mapping revealed a clear 2:1 relationship between common carp linkage groups and zebrafish chromosomes (Zhao et al 2013).…”

“…According to the study of karyotypic evolution and phylogenetic relationships in cyprinid fishes reported by Yu et al (1989), three main patterns of chromosome aberration were polyploidization, Robertsonian translocation, and chromosomal rearrangement. The karyotype (2n=100) of common carp and a clear 2:1 relationship between common carp linkage groups and zebrafish chromosomes demonstrated the whole genome duplication from the ancient genome of cyprinids (Zhao et al 2013). Moreover, chromosomal rearrangement, rather than Robertsonian translocation, was the main pattern of chromosome evolution after polyploidization in common carp.…”

“…Owing to the economical importance and the decline of nature populations of common carp, genetic and genomic studies had been performed during the past decades. Recently, two high-resolution genetic linkage maps for common carp have been published Zhao et al 2013). These high-resolution genetic linkage maps not only facilitate the identification of QTLs for superoxide dismutase , eye cross and eye diameter (Jin et al 2012), complex body shape (Zhang et al 2013b), and growth rate (Laghari et al 2013), but also provide a basic framework for G-C mapping in common carp.…”

“…In this study, we compared two high-resolution genetic linkage maps of common carp published recently and called them map Xu ) and map Zhao (Zhao et al 2013 Supplementary Fig. S1), and the rest linkage groups of map Xu had a strict one-to-one congruent relationship when compared with the map Zhao.…”

Quantitative trait loci for morphometric traits in multiple families of common carp (Cyprinus carpio)

“…Significant progress has been made in common carp genetics and genomics tools and resources over the last decade. A large number of polymorphic genetic markers (Ji et al, 2012;Xu et al, 2012a) have been developed, and several genetic linkage maps (Zheng et al, 2011;Zhao et al, 2013;Peng et al, 2016) have been constructed based on these markers. The genetic linkage maps have also been used to detect quantitative trait loci (QTLs) that affect the economic traits, including growth (Jin et al, 2012;Laghari et al, 2014a), biochemical (Xu et al, 2012b), and meat quality traits Kuang et al, 2015).…”